Archaea, Bacteria, and Viruses Chapter 19. Prokaryotes and Eukaryotes Terms introduced by Edouard Chatton in 1920s Based on microscopic observations ProkaryotesEukaryotes

Archaea, Bacteria, and Viruses

Chapter 19

Prokaryotes and Eukaryotes

• Terms introduced by Edouard Chatton in 1920s

• Based on microscopic observations

Prokaryotes Eukaryotes

“primitive nucleus” “true nucleus”

Lack clear nucleus and other inclusions

Clear nucleus and other inclusions

All organisms with cells that lack a nucleus

All organisms with cells that have a nucleus

Prokaryotes

• Carl Woese– Late 1970s– Proposed using the rRNA gene to create

universal tree of life• rRNA critical for proteins synthesis• Useful in determining evolutionary relationships

Three Domains

Domain Cell Type Description

Eukarya Eukaryotic Membrane bounded organelles, linear chromosomes

Archaea ProkaryoticFound in extreme environments, cell structure differs from members of Domain Bacteria

Bacteria Prokaryotic Ordinary bacteria, found in every habitat on earth, play major role as decomposers

Why Should A Botanist Study Prokaryotes?

• Reasons for studying prokaryotes– Many of the biochemical compounds,

enzymes, and metabolic pathways of plants also are found in prokaryotes.

– The evolutionary ancestors of plants were prokaryotes.

– Plants form ecological associations with prokaryotes.

Viruses

• Consist of– Either DNA or RNA– Protein coat

• Not prokaryotes• Noncellular cannot live independently• Discoveries obtained studying viruses can

be used to guide plant research

Prokaryotic Cell Structure

• Lacks internal membrane-enclosed organelles

• Surrounded by plasma membrane– Bacteria plasma membrane lipids similar to

those of eukaryotes– Archaeal plasma membrane lipids very

different• Held together by stronger bonds

Categories of Bacterial Cells

• Divided on basis of differential staining technique developed by Gram– Gram-negative cells– Gram-positive cells

Gram-positive Cells

• Capsule– Waxy polysaccharide– Protects some human pathogens from being

engulfed by immune system cells• Penicillin very effective against Gram-

positive cells– Inhibits formation of cell wall– Causes lysis of cells in hypotonic solutions

Comparison of Gram-positive and Gram-negative Cells

Gram-positive Gram-negative

Thick peptidoglycan cell wall Thin peptidoglycan cell wall

No second membrane – some have waxy polysaccharide capsule

Second membrane outside cell wall – lipopolysaccharide layer composed of phospholipids, polysaccharide, and protein

No periplasmic spacePeriplasmic space between cell wall and lipopolysaccharide layer

Shapes of Bacteria• Determined by cell wall

– Also functions to keep cell from bursting in hypotonic solution

– Composed of peptidoglycan• Shapes

– Cocci small, round cells– Bacilli rods– Vibrios bent or hooked rods– Spirilla helical forms– Stalked forms

Archaea

• Most have paracrystalline surface layer (S layer)– Composed of protein or glycoprotein– Sensitive to proteases and surfactants

• Some have outer covering of pseudopeptidoglycan

• Some have thick walls of polysaccharide• Typically lack an outer membrane

Bacterial DNA

• Typically a single, circular chromosome– Size in Escherichia coli

• 1.4 mm in length• Contains 4.6 million nucleotide pairs

• Not surrounded by nuclear envelope• Complexed with specific structural proteins

that organize it into loops• Localized in area called nucleoid

Archaeal DNA

• Chromosome complexed with histone proteins, similar to chromosomes of eukaryotes

Plasmids

• Accessory genes• Small circles of DNA approximately 2,000

to 200,000 nucleotide pairs in length• Can replicate independently of main

chromosome

Plasmids

• Examples of information carried by plasmid genes– Antibiotic resistance– Enzymes and structural proteins that transfer

copies of plasmid to Bacteria that do not have any

Plasmids

– F plasmid• Can incorporate itself into main chromosome• Contains genes for making tube called F pilus

– Connects its cell with another that lacks F plasmid– Transfers plasmid or chromosomal DNA from donor (cell

with pilus) to receiver cell – Transfer of DNA is called conjugation

Prokaryotic Ribosomes

• General composition and structure similar to those of eukaryotes– Two subunits made of RNA and protein

• Smaller than eukaryotic ribosomes• rRNAs of Archaea

– More similar to those of eukaryotes than Bacteria

Binary Fission

• Method of reproduction in prokaryotic cells• Differs from mitosis

– Prokaryotes lack microtubules therefore do not have spindle apparatus

Flagella• Used by many Bacterial and some Archaeal

cells for swimming• Formed of subunits of protein flagellin• Parts of flagellum

– Filament– Hook– Basal body

• Powered by basal body• In some instances can reverse swimming

direction

Pilus

• Extracellular organelle• Thin, hollow, nonmotile projection from cell• Proteins at ends of structure attach cell to

solid surfaces or to receptors on other cells

Cisternae

• Cisternae or thylakoid membranes• Found in some prokaryotic cells• Consist of flattened bladders than enclose

separate compartments within cytoplasm• Function

– in light reactions of photosynthesis in photosynthetic prokaryotes

– Energy storage

Endospores

• Means of survival for some prokaryotic cells

• Small, desiccated cells in condition of suspended animation

• Contain complete genome and needed chemicals for germination and growth when conditions improve

Endospores

• Resistant to many things such as boiling, oxidizing agents, antibiotic compounds

• Formation involves activation of special genes– In Bacteria such as Clostridium tetani

• Nucleoid and ribosomes surrounded by spore wall• Rest of cell degenerates

Endospores

– Actinobacteria• Form spores on vertical stalk• Spores blown to new sites by air currents

– Myxobacteria• Form sacs of endospores• Spores released when sac is hydrated

Nutritional Requirements of Prokaryotes

• Methods of obtaining carbon– Autotroph (“self-feeding) incorporate carbon

into organic molecules from inorganic sources– Heterotroph (“other feeding”) derive carbon

from breakdown of organic compounds


• Methods of deriving energy– Chemotroph (“chemical feeding”) obtain

energy from catalyzing inorganic reactions– Phototroph (“light feeding”) obtain energy

by absorbing light photons


Carbon source Energy source

Chemoautotroph Carbon from inorganic source incorporated into organic molecules

Catalyze inorganic reactions

Chemoheterotroph Carbon from breakdown of organic compounds

Catalyze inorganic reactions

Photoautotroph Carbon from inorganic source incorporated into organic molecules

Derive energy by absorbing light photons

Photoheterotroph Carbon from breakdown of organic compounds

Derive energy by absorbing light photons

Groups of Archaea

• Methanogens• Halophiles• Thermoacidophiles

Groups of Archaea

• Methanogens – Chemoautotrophs– Require anoxic environment to obtain energy– Produce methane

Reaction used by methanogens to derive energy:

CO2 + 4H2 CH4 + 2H2O

Groups of Archaea

• Halophiles– Live in saturated salt solutions– Some have little or no cell wall

• Will burst if moved from its normal environment– Example: Halobacterium halobium

• Unique type of photosynthesis• Photoreceptor – bacteriorhodopsin• No electron transport chain• Cannot make carbohydrates by reducing CO2 • Photoheterotroph

Groups of Archaea

• Thermoacidophiles– Live in hot, acidic environments– Optimum temperature is 70 to 75ºC with

maximum of 88ºC– Optimum pH is 2-3 (minimum pH 0.9)

Chemoheterotrophs

• Live on organic compounds of living or dead tissue or on excretions of other organisms

• Roles– May be harmful parasites

Chemoheterotrophs

– Can be beneficial• Compete for niches with potential pathogens• Gut chemoheterotrophs provide humans with

vitamin K• In dead tissue and on excretions, play role of

recycling carbon, nitrogen, and other elements

Chemoheterotrophs

• Some undergo fermentation– Lactobacillus

• Extensively studied bacterium, E. coli, is chemoheterotroph– Group Proteobacteria– Family Enterobacteriaceae

• Members live in soil and in intestines of animals• Often called enteric or coliform Bacteria

Chemoheterotrophs

– Presence of coliform Bacteria in water supplies indicates contamination with sewage

• Humans sewage carries pathogenic Bacteria and viruses

– Some strains of E. coli are not harmful, others produce toxins that cause severe infections

Examples of Chemoheterotrophs Genus Phylum Comment

Rhizobium Proteobacteria N2-fixing plant symbionts

Frankia Actinobacteria N2-fixing plant symbionts

Erwinia, Agrobacterium, Pseudomonas syringae Proteobacteria Plant pathogens

Desulfovibrio, Desulfomonas Proteobacteria Sulfate-reducing bacteria

Stigmatella, Chondromyces Proteobacteria Myxobacteria; colonial spore formers

Streptomyces Actinobacteria Antibiotic producers

Spirochaeta, Treponema Spirochaetes Long, thin, spiral-shaped; some pathogenic

Bacillus Firmicutes Aerobic endospore-formers

Escherichia Proteobacteria Enteric; model organism

**Rhodopseudomonas, Chromatium Proteobacteria Anaerobic phototrophs; purple nonsulfur

and purple sulfur groups

**Can be photoautotroph or chemoheterotroph

All of the above examples are in the Domain Bacteria.

Chemoautotrophs

• Examples– Lithotrophs

• Specialize in oxidation of inorganic compounds• Recycle nitrogen and sulfur

– Nitrogen and methane oxidizers– Methanogenic Archaea– Thermophilic and thermoacidophilic Archaea

Examples of Chemoautotrophs

Domain Genus Phylum Comment

Archaea Methanococcus, Methanospirillum Euryarchaeota

MethanogenicCO2 + 4H2 CH4 + 2H2O

ArchaeaThermoplasma

Euryarchaeota Thermoacidophile; grows at pH1-4 and 33-67ºC

ArchaeaPyrolobus Crenarchaeota Extreme thermophile; grows

up113ºC

BacteriaNitrosomonas, Nitrobacter, Methylomonas

Proteobacteria Nitrogen, methane oxidizers

Photoautotrophs

• Includes – Green sulfur Bacteria– Purple nonsulfur Bacteria– Cyanobacteria

• Light absorbing pigments– Bacteriochlorophyll

• Anaerobic phototrophs

– Chlorophyll• Cyanobacteria

• All reduce carbon to CO2

Examples of Photoautotrophs

Domain Genus Phylum Comment

Bacteria **Rhodopseudomonas, Chromatium Proteobacteria

Anaerobic phototrophs; purple nonsulfur and purple sulfur groups

Bacteria Chlorobium Chlorobi Anaerobic phototrophs; green sulfur group

Bacteria Anabaena, Nostoc, Prochloron Cyanobacteria Oxygen producers

**Can be either photoautotroph or chemoheterotroph

Photoautotrophs and Endosymbiosis

• Primitive cyanobacteria and chloroxybacteria thought to be evolutionary precursors of plastids of photosynthetic eukaryotes

• Strong evidence on similarities between light-harvesting complexes of– Cyanobacteria and red algae– Chloroxybacteria and green algae

Symbiotic Relationships Between Prokaryotes and Plants

• Rhizobium lives in soil– Synthesizes enzyme nitrogenase

• Converts N2 to ammonium (NH4+)

• Forms close mutualistic relationship with legumes– Plant contributes high energy carbohydrates and a

protected environment– Bacterium contributes nitrogenase and other enzymes– Both partners benefit from supply of fixed nitrogen


• Association occurs in special organs called root nodules

• Sequence of events in establishment of relationship– Root secretes attractive chemical– Chemical induces Rhizobium in vicinity to

swim toward root and begins induction of nitrogen fixation genes in Rhizobium


– Rhizobium enters at a root hair and moves inward through infection thread

– Rhizobium loses its cell wall and begins synthesizing nitrogen-fixing enzymes as it moves inward

– Bacteria reach root cortex – Bacteria are released from infection thread

into several cells– Bacteria without cell walls are now called

bacteroids


– Bacteroids become surrounded by special membrane called the peribacteroid membrane

– Chemicals secreted by Bacteria (or bacteroids) during formation of infection thread

• Induce cell division in root cortex and pericycle, forming nodule

• Induce synthesis of nodule proteins including leghemoglobin that buffers oxygen concentration in part of nodule where nitrogen is fixed


• Other examples of symbiotic nitrogen fixing Bacteria– Frankia – lives within cells of root nodules of

alder trees and other plants– Anabaena – association with water fern,

Azolla– Nostoc – invades cavities in gametophytes of

hornworts and specialized cells of cycads

Bacterial Parasites

• Parasitism– Symbiotic relationship in which one organism

benefits at the expense of the other• Plant pathogens divided into subgroups

called pathovars according to plants they infect

Bacterial Parasites

• Pathovars of Pseudomonas syringae cause– Wildfire disease of tobacco– Blights of beans, peas, and soybeans

• Pathovars of Erwinia amylovora cause– Fire blight of apple and pear

Bacterial Parasites

• Vectors for carrying Bacteria to uninfected plants include water, insects, humans, or other animals

• Bacteria enter plants through natural openings– Stomata– Lenticels– Hydathodes– Nectarthodes

Bacterial Parasites

• Some Bacterial pathogens can overwinter in dead tissue– Return to infect new plant tissue during next

growing season• Plant defenses against infecting bacteria

– Hypersensitivity response• Produce antibiotic compounds

– Phytoalexins directly kill some pathogenic cells– Hydrogen peroxide may restrict spread of infection by

causing necroses of adjacent plant cells

Viruses

• Subcellular parasites– Lack internal structures found in prokaryotic

and eukaryotic cells– Cannot reproduce on their own

• Invade host cells and use host’s metabolism to reproduce themselves

• Simple structure– Either DNA or RNA surrounded by protein

coat

Viruses

• Shape varies• Well-studied plant virus – tobacco mosaic virus• Plant viruses

– Too large to pass through cell wall– In nature, almost always spread by insects that pick

up viral particles as they chew or suck on infected plants and then transmit them to uninfected plants

– Mites and fungi can also infect plants with viruses when they enter plant cells

Viruses

• Viral infections usually do not kill plants• Infected plants usually stunted compared

to uninfected plants• Infection often causes changes in color or

shape of foliage

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Archaea, Bacteria, and Viruses Chapter 19. Prokaryotes and Eukaryotes Terms introduced by Edouard Chatton in 1920s Based on microscopic observations ProkaryotesEukaryotes